The MIKAIA® Cell x Gene App can be used to analyze FISH (or similar, e.g., RNAscope), CISH, or spatial transcriptomics scans, including Xenium by 10x Genomics. For Xenium data in particular, this app is the right choice, supporting three types of...
Chromogenic in situ hybridization (CISH) is used to detect specific DNA or RNA sequences in tissue samples. It uses enzyme-based staining rather than fluorescence (FISH), allowing for high-resolution imaging, quantification, and analysis under...
This MIKAIA® University app note demonstrates how to quickly and interactively train your own AI using just a few training annotations, all in a matter of minutes. In the app center, select the Segmentation AI Author App, click “+” to...
MIKAIA University is the central learning and resources portal for MIKAIA® users. It aims to illustrate how MIKAIA® can be used to make discoveries or automate quantitative analysis in Digital Pathology & Spatial Biology, offering app notes, FAQs, video tutorials, and more.
MIKAIA® AI Author used for Digital Pathology batch analysis
MIKAIA® is specifically designed for researchers in academia, CROs, biotech, pharma. One of the challenges is that researchers by design do unique things. For this reason, MIKAIA® apps do not represent individual side...
This article is based on a our presentation “IHC Cell Analysis — More than just Cell Counting: A proposed Workflow” at the European Conference for Digital Pathology (ECDP) 2024 in Vilnius, Lithuania...
MIKAIA® supports various I/O formats, find out which ones. Importable whole-slide-image file formats Format / VendorCommentsOME-TIFFBrightfield and fluorescence. Z-stacks and timelines supported (mutually-exclusive). No...
This MIKAIA® App Note shows how to quantify tumor in proximity to nerve fibers (perineural invasion) in a IHC duplex-stained tissue section, where nerves appear red (antigen: S100) and tumor brown (antigen:...
The first step to creating a supervised Digital Pathology AI is to annotate whole-slide-images. MIKAIA® uses various annotation concepts, and understanding these concepts will make your experience with MIKAIA® much...
About 20 % to 25 % of breast cancers depend on amplification and overexpression of the gene human epidermal growth factor receptor 2 (HER2). The HER2 overexpression status will initially be assessed by...
When designing a new immunohistochemistry (IHC) assay, a quantitative assessment of how it “responds” in different tissues of various organs is insightful and helps optimizing the assay in an objective way...
Tumor cells dynamically interact with their microenvironment to stimulate cancer development, progression, and metastasis. To understand the biology of the tumor-immune interactions, it is essential to identify tumoral...
In this MIKAIA® University application note, we guide you through the analysis of a common use case, coexpression of marker combinations in islets of Langerhans and surrounding tissue in a pancreas 4plex imaged with...
© Fraunhofer IIS · 2026
Volker Bruns
Michaela Benz
Nathalie Falk